Getting Unremediated PDB Files: Difference between revisions
New page: The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. ... |
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All files obtained from the World Wide Protein Data Bank since August 1, 2007, are remediated. Information about this remediation project can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page. | |||
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The data from before August 1, 2007 is available, as detailed [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904 here]. | |||
If your PDB file was published after August 1, 2007, it will not be available in unremediated form. | |||
The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. | The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. | ||
Use the interface at [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm Eric Martz's UMASS site] to get unremediated pdb files from the RCSB Protein Data Bank via FTP. | Use the interface at [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm Eric Martz's UMASS site] to get unremediated pdb files from the RCSB Protein Data Bank via FTP. | ||